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Cn matrix v3 #640
Cn matrix v3 #640
Commits on May 27, 2022
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Commits on Nov 28, 2023
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Commits on Dec 6, 2023
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Merge tag 'ctsm5.1.dev091' into cn-matrix_v3
This is a small changeset, which only adds the passing of a text based flag to FATES, that defines which soil decomposition method is active. This setting is needed by FATES, so that it can pass specific boundary conditions to CLM (and potentially ELM in the future). This change was necessitated because MIMICS requires a Nitrogen to lignin-carbon ratio in the litter flux, yet other decomposition schemes do not. Moreover, the generation of this boundary condition is not trivial, so it is worth it to avoid its computation if mimics is not on. This change should have NO impact on any tests. slevis resolved conflicts: cime_config/testdefs/ExpectedTestFails.xml cime_config/testdefs/testlist_clm.xml src/biogeochem/CNPhenologyMod.F90
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Commits on Dec 12, 2023
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Commits on Dec 15, 2023
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Merge tag 'ctsm5.1.dev092' into cn-matrix_v3
Refactor NutrientCompetition / CNAllocation to provide hooks for AgSys Major refactor of NutrientCompetition / CNAllocation to provide hooks for AgSys crop model: separates the NutrientCompetition modules into pieces based on (1) consolidating duplicate code between the Clm45 and FlexibleCN versions, and (2) separating pieces that will vs. won't be used for crop patches when running with the upcoming AgSys crop model. I have restored the old CNAllocationMod, with some of the responsibilities that it used to have. (I'm not sure it's appropriate to have the calculation of gpp and maint resp in CNAllocationMod, but I left it there because it has always been combined with the allocation code, including back when we had a separate CNAllocationMod.) slevis resolved conflicts: src/biogeochem/CNDriverMod.F90 src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 slevis important note: To resolve conflicts in the third (ie, last) of the above files, I checked with Will Wieder, and we agreed to not maintain a clm45 version of matrixcn.
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Commits on Dec 18, 2023
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Commits on Dec 19, 2023
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Merge tag 'ctsm5.1.dev093' into cn-matrix_slevis
Get FATES and carbon_only test-suite tests to pass with MIMICS active To pass with MIMICS active, FATES and carbon_only tests need calculations of: ligninNratioAvg and annsum_npp_col, both currently declared and calculated in CNVegCarbonFluxType.F90. ligninNratioAvg is a function of leafc_to_litter_patch, frootc_to_litter_patch, soilbiogeochem_cwdc_col, soilbiogeochem_cwdn_col, soilbiogeochem_decomp_cascade_ctransfer_col. I got both FATES and carbon_only tests to pass by declaring local copies (in MIMICS) of ligninNratioAvg and annsum_npp_col. slevis resolved conflicts: src/biogeochem/CNVegCarbonFluxType.F90 src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90
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Commits on Dec 20, 2023
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Merge tag 'ctsm5.1.dev095' into cn-matrix_v3
First pass at getting fates-sp mode to run without soil BGC Bring in externals updates that include adding AWS as a supported machine. Add a FatesSP compset and user-mod directory. Turn soil-BGC off when running FatesSP. Replace PGI tests on izumi with nvhpc tests on cheyenne. Fix an issue with a particular gnu compiler version in ch4Mod.F90 in DEBUG mode. Add some more threading tests for Fates. Start adding a prescribed-LAI tests for FatesSp Add a file to setup a python environment in conda for the python testing. Set line length for black to same as pylint (100). Add some extra excludes for black to the pylint checking. Paths for CIME python code was changed, which required changes to some CTSM python code. slevis resolved conflicts: cime_config/testdefs/ExpectedTestFails.xml cime_config/testdefs/testlist_clm.xml src/biogeochem/CNCStateUpdate1Mod.F90
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Merge tag 'ctsm5.1.dev096' into cn-matrix_v3
Update cime to fix DAE issue modify_neon issue When FatesSp is on, make soil_decomp None by default slevis resolved conflicts: cime_config/testdefs/ExpectedTestFails.xml
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Merge tag 'ctsm5.1.dev099' into cn-matrix_v3
This set of changes 1) allows FATES to dictate the number of patches on the naturaly vegetated land unit and 2) is compatible with a version of FATES that updates the parameter file format (changes in parameter naming and parameter set). Efforts were made to adhere to the system of how patches are looped and loop bounds are defined. There is interaction with the reading of the surface file, which previously dictated all patch counts based on the number of PFTs in the file. FATES-SP and biogeography preserves the ability to use surface file weighting factors associated with PFTs and CFTs to drive area fractions in FATES. This change is motivated by FATES-side updates to the parameter file, which includes new settings where the user can control the number of primary "fates_maxpatch_primary" and secondary "fates_maxpatch_secondary" patches. Users should also be aware of a new namelist setting "use_fates_tree_damage" which defaults to false (inoperative). slevis resolved conflicts: bld/unit_testers/build-namelist_test.pl
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Commits on Dec 22, 2023
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Merge tag 'ctsm5.1.dev100' into cn-matrix_v3
First Commit of CN Matrix Solution: Start bringing in the use_matrixcn and use_soil_matrixcn control options for the Carbon/Nitrogen BGC model using the matrix solution methodology developed by Dr. Yiqi Luo and his EcoLab members: Drs. Xingjie Lu, Yuanyuan Huang and Zhengguang Du, at Northern Arizona University Work on Anomaly forcing for SSEP scenarios: Do some work on anomoly forcing for SSP scenarios. Update the script in tools/contrib to work with the latest data and replicate results of Keith Oleson and Sean Swenson. Add some test cases for it. Python Environment Management using Conda: More work on the manage_python_env script to setup the "ctsm_py" conda environment. This now works for UCAR machines (such as cheyenne and casper) as well as CGD machines (like izumi). This script can also be called for tools, and the test tools mechanism is now using it rather than ncar_pylib. ./manage_python_env SCAM Fix: Add checkimport method for CMEPS so that single-column case can work with SCAM, from Jim Edwards. Black Formatter for Python Code: Run "black" python code reformatter on all code under the "python" directory. Add the commits to .git-blame-ignore-revs so they can be ignored when "git blame" is used, if you add this to each clone where you want this to apply: git config blame.ignoreRevsFile .git-blame-ignore-revs You can do it for your worktrees, but since the file only applies to CTSM for ctsm5.1.dev100 and forward, you'll need to do it for each CTSM clone seperately. Also there is now a github action that checks that python code under the "python" subdirectory is black clean. If it's not the action will fail and send you an email about it. Make Map Data Fix: Simple fix from Sam Rabin. Fix for DISPLA on History Output: Fix from Keith Oleson to set history output for DISPLA (displa_patch) to zero when vegetation is buried by snow. slevis resolved conflicts: bld/CLMBuildNamelist.pm bld/namelist_files/namelist_defaults_ctsm.xml bld/unit_testers/build-namelist_test.pl cime_config/testdefs/testlist_clm.xml src/biogeochem/CNAllocationMod.F90 src/biogeochem/CNCStateUpdate1Mod.F90 src/biogeochem/CNDriverMod.F90 src/biogeochem/CNNStateUpdate1Mod.F90 src/biogeochem/CNPhenologyMod.F90 src/biogeochem/CNVegCarbonFluxType.F90 src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 slevis had to restore many other files for which git replaced the matrixcn mods with dev100's matrixcn stubs. slevis is testing the code with SMS_Ln9.ne30pg2_ne30pg2_mg17.I2000Clm50BgcCrop.cheyenne_intel.clm-clm50cam6LndTuningMode and getting a column cbalance error at the moment.
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Commits on Dec 26, 2023
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Merge tag 'ctsm5.1.dev118' into cn-matrix_v3
Use conda environment rather than ncar_pylib with the fsurdat_modifier system test Reason: ncar_pylib is going away soon. slevis resolved conflicts: bld/unit_testers/build-namelist_test.pl cime_config/testdefs/testlist_clm.xml src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90
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Commits on Dec 27, 2023
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Merge tag 'ctsm5.1.dev119' into cn-matrix_v3
Get gross unrepresented land use transitions working in CLM5.1. This is additional optional data added to the landuse.timeseries files for transient simulations. The current landuse.timseries files have this data, but it's set to zero. This data will be part of the CTSM5.2 surface dataset (that is upcoming) and be on by default for clm5_3 physics. slevis resolved conflict: bld/unit_testers/build-namelist_test.pl
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Commits on Dec 28, 2023
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Commits on Dec 29, 2023
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Merge tag 'ctsm5.1.dev133' into cn-matrix_v3
FATES API update to facilitate fates refactor This updates a number of FATES type names and module use statements which correspond with a refactoring effort that moves FATES patches and cohorts into their own respective modules. With the FATES update is a minor science update, so there are changes to answers for FATES. This also incorporates a minor update to a more recent version of the ccs config external. slevis resolved conflicts: bld/unit_testers/build-namelist_test.pl cime_config/buildnml src/biogeochem/CNVegCarbonFluxType.F90
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Commits on Dec 30, 2023
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Merge tag 'ctsm5.1.dev134' into cn-matrix_v3
Migration of FATES to share normal soil BGC call sequence and functionality This set of changes enables the normal soil biogeochemistry that is used for CN, to be used for FATES as well. FATES had been using a simplified subset of soil biogeochemistry in its own module. This change required coordination of litter flux and methane boundary conditions from FATES to CLM. CNVEG datastructures were given trivial allocation (of size one on index zero) to prevent inappropriate use of CNVEG datastructures while FATES is active. Note that now the carbon balance checking for the soil is now active when FATES is active. Various accomodations have also been put in place to enable nitrogen cycling between the two models. slevis resolved conflicts: bld/unit_testers/build-namelist_test.pl src/biogeochem/CNCStateUpdate1Mod.F90 src/biogeochem/CNDriverMod.F90 src/biogeochem/CNVegCarbonStateType.F90 src/biogeochem/CNVegNitrogenStateType.F90 src/biogeochem/CNVegetationFacade.F90 src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90
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Merge commit '46cbf4b' into cn-matrix_v3
because I updated 2 local copies of cn-matrix_v3 at the same time
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Corrections for model to build and a test to pass
Used this one for testing: SMS_D.1x1_brazil.I1850Clm51BgcCrop.cheyenne_gnu.clm-mimics_matrixcn
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Commits on Dec 31, 2023
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Commits on Jan 2, 2024
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Merge tag 'ctsm5.1.dev159' into cn-matrix_v3
Various BFB fixes and updates Purpose/description of changes ------------------------------ the default comes in a later tag (slevis) Regular and python testing passed. Does not change answers relative to dev158. slevis resolved conflicts UNTESTED: bld/unit_testers/build-namelist_test.pl cime_config/testdefs/testlist_clm.xml src/biogeochem/CNPhenologyMod.F90 src/biogeochem/CNVegNitrogenFluxType.F90 src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 AND I will still look for potential additional inconsistencies that I may need to resolve
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Merge commit '107f854' into cn-matrix_v3
because I updated 2 parallel local copies of cn-matrix_v3
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Commits on Jan 3, 2024
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Commits on Mar 7, 2024
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Merge tag 'ctsm5.1.dev162' into cn-matrix_v3
Improvements to processing of crop calendar files In python/ctsm/crop_calendars/, process_ggcmi_shdates.py and regrid_ggcmi_shdates.py are used to convert the raw GGCMI crop calendar files into CTSM-compatible versions. This update fixes some bugs, removes dependencies on the nco utilities, enables the use of surface datasets as template files (in addition to the existing ability to use CTSM output files), and standardizes things for consistency with other CTSM Python tools.
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Commits on Mar 12, 2024
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Merge tag 'ctsm5.1.dev163' into cn-matrix_v3
Adds capability for cropland soil tillage and post-harvest residue removal. Tillage: This PR brings in the tillage code written by Sam Levis and Michael Graham and used in Graham et al. (2021, ERL, doi:10.1088/1748-9326/abe6c6). Low- and high-intensity tillage here work by increasing the decomposition rate of different soil carbon pools. These "decomposition multipliers" vary based on soil pool and how long it's been since the crop was planted; they are set with new paramfile variables till_decompk_multipliers and mimics_till_decompk_multipliers. Note that tillage is off by default. Residue removal: Adds a parameter hat represents what fraction of post-harvest crop residues (stems and leaves) should be removed to the crop product pool rather than being transferred to litter. slevis resolved conflicts: src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90
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Commits on Mar 19, 2024
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Merge tag 'ctsm5.1.dev174' into cn-matrix_v3
Changes to improve vegetation health at high latitudes Details in PR ESCOMP#2348 slevis resolved conflicts: bld/unit_testers/build-namelist_test.pl
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Commits on Mar 27, 2024
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Rename isspinup -> spinup_matrixcn, is_outmatrix -> hist_wrt_matrixcn…
…_diag Ran aux_clm on derecho and got expected results
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Merge tag 'ctsm5.1.dev175' into cn-matrix_v3
Merge b4bdev 20240321
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Merge tag 'ctsm5.1.dev176' into cn-matrix_v3
Merge b4b-dev slevis resolved conflicts: bld/unit_testers/build-namelist_test.pl
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Merge tag 'ctsm5.2.001' into cn-matrix_v3
Merge b4b-dev Some fixes for run_neon that came up in ctsm5.1.dev172. Small bug fix for units of vector format hillslope hydrology. Start adding PLUMBER2 users-mods (NOT functional) slevis resolved conflicts: .git-blame-ignore-revs bld/namelist_files/namelist_defaults_ctsm.xml bld/unit_testers/build-namelist_test.pl cime_config/config_compsets.xml cime_config/testdefs/testlist_clm.xml
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Commits on May 15, 2024
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Merge tag 'ctsm5.2.005' into cn-matrix_v3
ix clm6_0 defaults and CESM testing issues, add tests to detect these problems Fix the clm6_0 defaults that were incorrect in ctsm5.2.0. The use-cases needed to be changed to handle clm6_0. And clm6_0 wasn't handled in the merge of ctsm5.1.dev174 for the two new settings. Simplified the use-cases which should help prevent these problems in the future. use_init_interp will be set for ctsm5.1 finidat files. Fix some testing. mksurfdata_esmf and the MKSUIRFDATA test didn't work in a CESM checkout. build-namelist unit tests weren't going over the use-cases. Also started adding some tests to go over finidat files, but didn't yet capture all of them. Add some scripts to compare namelists in order to detect namelist issues for physics version updates, and more easily see namelist changes in one place (bld/unit_testers/cmp_baseline_lnd_in_files, bld/unit_testers/compare_namelists). Add some tests to detect issues in CESM and CAM testing (add more tests for cam6.0 forcing, add new IHistClm60BgcCropG compset). Add a NoAnthro compset to the ctsm_sci testing. Add I1850Clm60Sp test for f09 and f19 to ctsm_sci. Change NoAnthro compsets to use RTM rather than MOSART. Add science support to some clm6_0 compsets, as was obvious. slevis resolved conflicts: bld/unit_testers/build-namelist_test.pl cime_config/testdefs/ExpectedTestFails.xml cime_config/testdefs/testlist_clm.xml
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Commits on May 16, 2024
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Commits on May 31, 2024
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Merge tag 'ctsm5.2.007' into cn-matrix_v3
Rm manage_externals and update documentation accordingly Fixes ESCOMP#2537 Remove manage_externals stuff from run_sys_tests Fixes ESCOMP#2536 Update documentation for git-fleximod Fixes ESCOMP#2467 Remove references to cheyenne from the testlist slevis resolved conflicts: bld/unit_testers/build-namelist_test.pl cime_config/testdefs/ExpectedTestFails.xml cime_config/testdefs/testlist_clm.xml
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Merge tag 'ctsm5.2.011' into cn-matrix_v3
Merge b4b-dev slevis resolved conflicts: .git-blame-ignore-revs bld/unit_testers/build-namelist_test.pl src/biogeochem/CNDriverMod.F90 src/main/controlMod.F90
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Merge tag 'ctsm5.2.012' into cn-matrix_v3
Relax tolerance for truncating small snocan values in CanopyFluxes See the PR ESCOMP#2457 for details.
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Merge remote-tracking branch 'escomp/master' into cn-matrix_v3
slevis resolved conflicts: bld/unit_testers/build-namelist_test.pl
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